Nextflow workflow report

[peaceful_yalow]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 102.

The full error message was:

Error executing process > 'STAR_Fusion (268)'

Caused by:
  Process `STAR_Fusion (268)` terminated with an error exit status (102)

Command executed:

  set -eou pipefail
  
  STAR --genomeDir $PWD/ctat_genome_lib_build_dir/ref_genome.fa.star.idx 			--runThreadN 8 			--readFilesIn SJCBF022_D.RNA-Seq_r1.fastq.gz SJCBF022_D.RNA-Seq_r2.fastq.gz 			--outFileNamePrefix SJCBF022_D.RNA-Seq_ 			--outReadsUnmapped None 			--twopassMode Basic 			--twopass1readsN -1 			--readFilesCommand "gunzip -c" 			--outSAMunmapped Within 			--outSAMtype BAM SortedByCoordinate 			--limitBAMsortRAM 63004036730 			--outSAMattributes NH HI NM MD AS nM jM jI XS 			--chimSegmentMin 12 			--chimJunctionOverhangMin 12 			--chimOutJunctionFormat 1 			--alignSJDBoverhangMin 10 			--alignMatesGapMax 100000 			--alignIntronMax 100000 			--alignSJstitchMismatchNmax 5 -1 5 5 			--outSAMattrRGline ID:GRPundef 			--chimMultimapScoreRange 3 			--chimScoreJunctionNonGTAG -4 		  --chimMultimapNmax 20 			--chimNonchimScoreDropMin 10 			--peOverlapNbasesMin 12 			--peOverlapMMp 0.1 			--chimFilter banGenomicN
  
  
  /usr/local/src/STAR-Fusion/STAR-Fusion --genome_lib_dir $PWD/ctat_genome_lib_build_dir 	  	--chimeric_junction "SJCBF022_D.RNA-Seq_Chimeric.out.junction" 			--left_fq SJCBF022_D.RNA-Seq_r1.fastq.gz 			--right_fq SJCBF022_D.RNA-Seq_r2.fastq.gz 	  	--CPU 8 	  	--FusionInspector inspect 	  	--examine_coding_effect 	  	--denovo_reconstruct 	  	--output_dir SJCBF022_D.RNA-Seq_
  
  
  echo ----------------------------------------
  echo "list all output files in /home/jlsmith3/scripts/STAR-fusion-NF"
  ls -1 $PWD
  
  echo -----------------------------------------
  echo "list all output files in sample directory"
  ls -1 SJCBF022_D.RNA-Seq_

Command exit status:
  102

Command output:
  Sep 28 02:27:19 ..... started STAR run
  Sep 28 02:27:19 ..... loading genome
  Sep 28 02:27:37 ..... started 1st pass mapping
  Sep 28 02:57:11 ..... finished 1st pass mapping
  Sep 28 02:57:12 ..... inserting junctions into the genome indices
  Sep 28 03:01:02 ..... started mapping
  Sep 28 03:44:19 ..... finished mapping
  Sep 28 03:44:22 ..... started sorting BAM

Command error:
  
  EXITING because of fatal ERROR: not enough memory for BAM sorting: 
  SOLUTION: re-run STAR with at least --limitBAMsortRAM 64523905173
  Sep 28 03:44:22 ...... FATAL ERROR, exiting

Work dir:
  s3://fh-pi-meshinchi-s/SR/work/95/fc9128ddca0410904344919934facf

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
25-Sep-2020 18:22:33 - 27-Sep-2020 20:44:47 (duration: 2d 2h 22m 14s)
  491 succeeded  
  0 cached  
  0 ignored  
  10 failed  
Nextflow command
nextflow run -c /home/jlsmith3/nextflow.config STAR_Fusion.nf --sample_sheet sample_sheets/st.jude_sample_sheet.txt --genome_lib 's3://fh-pi-meshinchi-s/SR/Reference_Data/GRCh37_gencode_v19_CTAT_lib_Oct012019/ctat_genome_lib_build_dir/' --output_folder 's3://fh-pi-meshinchi-s/SR/starfusion/' -with-report STAR-Fusion_St.Jude_report.html -work-dir 's3://fh-pi-meshinchi-s/SR/work' -cache TRUE -process.queue cpu-spot-50 ' #temporary' bc spot-30 is not really working
CPU-Hours
15'741.2 (2.9% failed)
Launch directory
/home/jlsmith3/scripts/STAR-fusion-NF
Work directory
s3://fh-pi-meshinchi-s/SR/work
Project directory
/home/jlsmith3/scripts/STAR-fusion-NF
Script name
STAR_Fusion.nf
Script ID
50215d3e1bcdea339a046d7127b8243e
Workflow session
e25f3dfe-aca8-4a04-aea4-72928f6a284f
Workflow profile
standard
Nextflow version
version 20.04.1, build 5335 (03-05-2020 19:37 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)